Are you looking at stopping over on MEL, or do you just want to route SYD-PER via MEL?
If the former, then it doesn't matter that they are all on seperate PNR's.
If the latter - SYD-X/MEL-PER then if you request SYD-PER then sometimes the system will throw you an itinerary via MEL - sometimes not.
Unless you are after a Red E-deal (N class) it wil make no difference whether you book it online or over the phone. In fact, over the phone can often get some combinations the computer won't give you/
If you ARE after a Red E-deal, consider a Red Deal instead - booked in O class, about 8% more expensive, but greater availability and bookable over the phone.
Dave